|
| Status |
Public on Mar 17, 2017 |
| Title |
LNCaP_OxBis_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
LNCaP cell line DNA
|
| Organism |
Homo sapiens |
| Characteristics |
tissue type: LNCaP clone
passage: 73
|
| Treatment protocol |
no treatment
|
| Growth protocol |
Adult Brain Frontal Lobe genomic DNA from a single donor was purchased from Banksia Scientific Company (Bulimba, Australia, cat no D1234035). LNCaP cells were cultured as desribed previously [Song JZ et al, Oncogene 2002, 21:1048-1061].
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA from LNCaP cells was exctracted using QIAamp DNA Mini kit (Qiagen, USA)
CEGX TrueMethyl® WG
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
LNCaP clone FGC(ATCC® CRL-1740™). Androgen-sensitive human prostate adenocarcinoma cells derived from metastatic site: left supraclavicular lymph node
bigTable_LNCaP.tsv.gz
|
| Data processing |
Bisulphite reads were aligned to the human genome using version 1.2 of an internally developed pipeline, publicly available for download from http://github.com/astatham/Bisulphite_tools.
Adaptor sequences and poor quality bases were removed using Trimgalore (version 0.2.8, http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) in paired-end mode with default parameters.
Bismark v0.8.326 was then used to align reads to hg19 using the parameters “-p 4 –bowtie2 –X 1000 –unmapped –ambiguous –gzip –bam”
PCR duplicates were removed using Picard v1.91 (http://broadinstitute.github.io/picard)
Count tables of the number of methylated and unmethylated bases sequenced at each CpG site in the genome were constructed using bismark_methylation_extractor with the parameters “-p –no_overlap –ignore_r2 4 –comprehensive –merge_non_CpG –bedgraph –counts –report –gzip –buffer_size 20G”
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited
|
| |
|
| Submission date |
Jan 31, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Ksenia Skvortsova |
| E-mail(s) |
[email protected]
|
| Phone |
478135210
|
| Organization name |
Garvan Institute
|
| Department |
Genomics and Epigenetics
|
| Lab |
Developmental Epigenomics
|
| Street address |
384 Victoria St, Darlinghurst
|
| City |
Sydney |
| State/province |
NSW |
| ZIP/Postal code |
2010 |
| Country |
Australia |
| |
|
| Platform ID |
GPL20795 |
| Series (2) |
| GSE94331 |
Comprehensive evaluation of genome-wide 5-hydroxymethylcytosine profiling approaches in human DNA [BiSulfite-seq] |
| GSE94368 |
Comprehensive evaluation of genome-wide 5-hydroxymethylcytosine profiling approaches in human DNA |
|
| Relations |
| BioSample |
SAMN06285123 |
| SRA |
SRX2529941 |
